When you set up the Clients in your mission, there are four buttons on the Client information box on the right side of the mission editor screen... the buttons are kind of in the middle of the Client panel.
The left most button is the Waypoints editor, the next is the Weapons loadout. You can choose a default loadout or Copy one of those to a new loadout with your own assigned loadout name.
If the base you are taking off from has support capability, you can contact the ground crew and change the assigned loadout to something else that is available from the menu.
Some time ago I tried custom loadouts but did not get it to work. I'm not even sure that if I had a custom loadout list on my computer if other Clients in one of my missions would also be able to see that custom list. I stick with the default stuff, no mods here.
I'm not familiar with the "flight planner" that you mentioned above.